Platform Design Info for Affymetrix FinGene-1_0-st.

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

Most analyses of Affymetrix GeneChip data (including tranditional 3 arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3 arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Platform Design Info for NimbleGen feinberg_mm8_me_hx1.

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

Platform Design Info for The Manufacturer's Name Mu11KsubB.

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Platform Design Info for Affymetrix DroGene-1_1-st.

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Platform Design Info for Affymetrix RaGene-1_1-st-v1.

Platform Design Info for The Manufacturer's Name HG_U95A.

Platform Design Info for Affymetrix CHOGene-2_1-st.

Platform Design Info for The Manufacturer's Name Soybean.

Platform Design Info for Affymetrix miRNA-3_0.

Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.

Platform Design Info for Affymetrix RUSGene-1_0-st.

Platform Design Info for Affymetrix RCnGene-1_1-st.

Platform Design Info for Affymetrix Clariom_S_Rat.

Platform Design Info for Affymetrix FinGene-1_1-st.